Cattle are commonly treated with antibiotics that may survive digestion and promote antibiotic resistance when manure or composted manure is used as a soil amendment for crop production. This study was conducted to determine the effects of antibiotic administration and soil amendment practices on microbial diversity and antibiotic resistance of bacteria recovered from the surfaces of lettuce and radishes grown using recommended application rates. Vegetables were planted in field plots amended with raw manure from antibiotic-treated dairy cows, composted-manure from cows with different histories of antibiotic administration, or a chemical fertilizer control (12 plots, n=3). Culture-based methods, 16SrDNA amplicon sequencing, qPCR and shot-gun metagenomics were utilized to profile bacteria and characterize the different gene markers for antibiotic resistance. Culture-based methodologies revealed that lettuce grown in soils amended with BSAs had significantly larger clindamycin resistant populations compared to control conditions. Growth in BSAs was associated with significant changes to the bacterial community composition of radish and lettuce. Total sul1 copies were 160X more abundant on lettuce grown in manure and total tet(W) copies were 30X more abundant on radishes grown in manure. Analysis of shotgun metagenomic data revealed that lettuce grown in manure-amended soils possessed resistance genes for three additional antibiotic classes compared to other treatments. This study demonstrates that raw, antibiotic-exposed manure may alter microbiota and the antibiotic resistance genes present on vegetables. Proper composting of BSAs as recommended by the U.S. Department of Agriculture and Environmental Protection Agency is recommended to mitigate the spread of resistance to vegetable surfaces. / MSLFS / Antibiotics are drugs responsible for killing infectious diseases in both humans and animals. In cows, antibiotics are frequently used when they get infections in their udders. These drugs can be excreted through manure and urine and end up in the environment. Manure or composted manure is often applied as a soil amendment for crop production. The presence of antibiotics in soil may promote antibiotic resistance, meaning bacteria that carry antibiotic resistance genes (ARGs) are capable of surviving exposure to drugs that would normally kill them. Such bacteria may eventually pass their ARGs to pathogens, which then could no longer be treated effectively by antibiotics when there is an infection. Thus, there is concern that overuse of antibiotics in agriculture can contribute to reduced effectiveness of antibiotics and the growing global antibiotic resistance health crisis. This study sought to determine if prior antibiotic administration affected the antibiotic resistance of bacteria found on the surfaces of vegetables grown in soil amended with manure or compost from dairy cows. Lettuce and radishes were grown in the field in plots amended with raw manure from antibiotic-treated dairy cows, compost from cows with different histories of antibiotic administration, or a chemical fertilizer control. Mature vegetables were harvested and used to enumerate antibiotic-resistant bacterial colonies. Additionally, the 16S rRNA gene, which is a ubiquitous gene found in all bacteria, was sequenced to identify the kinds of microbes that colonized the radish and lettuce surfaces when grown under the different conditions. DNA was extracted from the bacteria collected from the vegetable surfaces to and different methods were used to identify the kinds of ARGs present and to which kinds of antibiotics they encode resistance. The results of the study indicated that raw, antibiotic-exposed manure may increase the bacteria found on vegetables in addition to their ARGs. Proper composting of manure, as recommended by the U.S. Department of Agriculture (USDA) and the Environmental Protection Agency (EPA), is recommended to mitigate resistance and control microbial populations on fresh vegetables.

As áreas alagáveis naturais representam a mais importante fonte não-antropogênica de metano (CH4), com emissões estimadas entre 177 a 284 Tg ano-1, representando de 26 a 42% das emissões globais de CH4. A bacia do Rio Amazonas cobre uma grande porção dos trópicos úmidos, e a rede de drenagem deste rio excede a extensão de mais de um milhão de quilômetros quadrados. As grandes várzeas da bacia Amazônica são as maiores fontes naturais de CH4 desta região e estima-se que sua contribuição para as emissões totais de áreas alagadas no mundo seja na ordem de 5%. O CH4 produzido nas zonas anaeróbicas dos sedimentos por arquéias metanogênicas pode ser oxidado a CO2 pelos microrganismos metanotróficos. Com base na hipótese de que o fluxo de CH4 se altera sazonalmente em áreas alagáveis e que a microbiota presente está diretamente relacionada a esse processo, o presente estudo teve como objetivo geral avaliar a dinâmica dos genes funcionais envolvidos no ciclo do CH4 em épocas contrastantes, correlacionando com o fluxo do gás, variáveis ambientais e perfil taxonômico de Bacteria e Archaea em sedimentos de três áreas alagáveis e solo de floresta primária, da Amazônia Oriental (Belterra e Santarém-PA). Foram realizadas amostragem de gases, sedimentos e solo em duas épocas contrastantes (maio e outubro de 2016 - cheia e seca), para determinação da concentração de CH4 retido no sedimento durante a época cheia, cálculo do fluxo de CH4 durante a época seca, análises físico-químicas e extração de DNA dos sedimentos e solo para realização da qPCR dos genes funcionais mcrA e pmoA e dos genes marcadores filogenéticos 16S rRNA de Bacteria e Archaea, e sequenciamento do gene 16S rRNA de Bacteria e Archaea. A partir das amostragens de gases, foi possível observar que as áreas alagáveis possuem potencial de atuarem como fonte de CH4 durante a época cheia, e como fonte ou dreno de metano durante a época seca, confirmado pelas análises de qPCR, uma vez que a abundância do gene pmoA aumenta durante a época seca. Já no solo de floresta, o gene mcrA foi considerado como não detectado, portanto, a floresta pode ser considerada somente como potencial dreno de CH4. O estimador ACE e o índice Shannon mostraram que os sedimentos de áreas alagáveis possuem maior riqueza e diversidade de Bacteria e Archaea quando comparados ao solo de floresta. Todas as áreas apresentaram perfis taxonômicos do domínio Bacteria semelhantes, porém, a grande diferença entre as comunidades está relacionada ao domínio Archaea. A comunidade de arqueias no solo de floresta é majoritariamente composta por representantes do filo Thaumarchaeota. O solo de floresta apresentou baixa abundância dos filos potencialmente produtores de CH4, Bathyarchaeota e Euryarchaeota, e o contrário foi observado nas áreas alagáveis. Os dados gerados no presente estudo incentivam a continuidade de trabalhos relacionados ao ciclo do CH4 em áreas alagáveis da bacia Amazônica, incluindo investigações acerca do papel do filo Bathyarchaeota nessas áreas, principalmente em relação ao ciclo do CH4 / Natural wetlands represent the most important non-anthropogenic source of methane (CH4), with emissions estimated of 177-284 Tg year-1, accounting for 26-42% of global CH4 emissions. The Amazon basin covers a large portion of the humid tropics, and the drainage network of this river exceeds the extent of more than one million square kilometers. The wetlands of the Amazon basin are the largest natural sources of CH4 in this region and it is estimated that their contribution to the total emissions of wetlands in the world is around 5%. The CH4 produced in the anaerobic zones of the sediments by methanogenic archaea can be oxidized to CO2 by the methanotrophic microorganisms. Based on the hypothesis that methane flux changes seasonally in wetlands and its microbiota is directly related to this process, this research has the main objective to evaluate the dynamics of the functional genes involved in the CH4 cycle in contrasting seasons, correlating with the CH4 flux, environmental variables and taxonomic profile of Bacteria and Archaea in three wetlands and one primary forest of the Eastern Amazon (Belterra and Santarém-PA). The sampling of gas, sediments and soil was performed in May and October 2016 (wet and dry seasons) to determine the concentration of CH4 retained in the sediment in the wet season, measurement of CH4 flux in the dry season, physicochemical properties and molecular analysis (qPCR of the mcrA, pmoA functional genes and phylogenetic marker genes 16S rRNA of Bacteria and Archaea and sequencing of the 16S rRNA gene of Bacteria and Archaea). From gas samplings, it was possible to observe that wetlands have the potential to act as source of CH4 during the wet season, and as a source or drain of CH4 during the dry season, confirmed by qPCR analyzes, due the abundance increases of the pmoA gene during the dry season. In the forest soil, the mcrA gene was not detected, therefore, the forest could be considered only as CH4 drain potential. The ACE estimator and the Shannon index showed that the sediments of wetlands have higher richness and diversity of Bacteria and Archaea when compared to the forest soil. All areas presented similar taxonomic profiles of Bacteria, however, the main difference between the communities is related to the Archaea. The archaeal community in the forest soil is mostly composed of representatives of the phylum Thaumarchaeota. The forest soil presented low abundance of the phyla with potential CH4 producers, Bathyarchaeota and Euryarchaeota, however the opposite was observed in the wetlands. The data generated in the present study encourage the continuity of work related to the CH4 cycle in wetlands of the Amazon basin, including investigations about the role of the Bathyarchaeota phylum in these areas, especially in relation to the CH4 cycle

As áreas alagáveis naturais representam a mais importante fonte não-antropogênica de metano (CH4), com emissões estimadas entre 177 a 284 Tg ano-1, representando de 26 a 42% das emissões globais de CH4. A bacia do Rio Amazonas cobre uma grande porção dos trópicos úmidos, e a rede de drenagem deste rio excede a extensão de mais de um milhão de quilômetros quadrados. As grandes várzeas da bacia Amazônica são as maiores fontes naturais de CH4 desta região e estima-se que sua contribuição para as emissões totais de áreas alagadas no mundo seja na ordem de 5%. O CH4 produzido nas zonas anaeróbicas dos sedimentos por arquéias metanogênicas pode ser oxidado a CO2 pelos microrganismos metanotróficos. Com base na hipótese de que o fluxo de CH4 se altera sazonalmente em áreas alagáveis e que a microbiota presente está diretamente relacionada a esse processo, o presente estudo teve como objetivo geral avaliar a dinâmica dos genes funcionais envolvidos no ciclo do CH4 em épocas contrastantes, correlacionando com o fluxo do gás, variáveis ambientais e perfil taxonômico de Bacteria e Archaea em sedimentos de três áreas alagáveis e solo de floresta primária, da Amazônia Oriental (Belterra e Santarém-PA). Foram realizadas amostragem de gases, sedimentos e solo em duas épocas contrastantes (maio e outubro de 2016 - cheia e seca), para determinação da concentração de CH4 retido no sedimento durante a época cheia, cálculo do fluxo de CH4 durante a época seca, análises físico-químicas e extração de DNA dos sedimentos e solo para realização da qPCR dos genes funcionais mcrA e pmoA e dos genes marcadores filogenéticos 16S rRNA de Bacteria e Archaea, e sequenciamento do gene 16S rRNA de Bacteria e Archaea. A partir das amostragens de gases, foi possível observar que as áreas alagáveis possuem potencial de atuarem como fonte de CH4 durante a época cheia, e como fonte ou dreno de metano durante a época seca, confirmado pelas análises de qPCR, uma vez que a abundância do gene pmoA aumenta durante a época seca. Já no solo de floresta, o gene mcrA foi considerado como não detectado, portanto, a floresta pode ser considerada somente como potencial dreno de CH4. O estimador ACE e o índice Shannon mostraram que os sedimentos de áreas alagáveis possuem maior riqueza e diversidade de Bacteria e Archaea quando comparados ao solo de floresta. Todas as áreas apresentaram perfis taxonômicos do domínio Bacteria semelhantes, porém, a grande diferença entre as comunidades está relacionada ao domínio Archaea. A comunidade de arqueias no solo de floresta é majoritariamente composta por representantes do filo Thaumarchaeota. O solo de floresta apresentou baixa abundância dos filos potencialmente produtores de CH4, Bathyarchaeota e Euryarchaeota, e o contrário foi observado nas áreas alagáveis. Os dados gerados no presente estudo incentivam a continuidade de trabalhos relacionados ao ciclo do CH4 em áreas alagáveis da bacia Amazônica, incluindo investigações acerca do papel do filo Bathyarchaeota nessas áreas, principalmente em relação ao ciclo do CH4 / Natural wetlands represent the most important non-anthropogenic source of methane (CH4), with emissions estimated of 177-284 Tg year-1, accounting for 26-42% of global CH4 emissions. The Amazon basin covers a large portion of the humid tropics, and the drainage network of this river exceeds the extent of more than one million square kilometers. The wetlands of the Amazon basin are the largest natural sources of CH4 in this region and it is estimated that their contribution to the total emissions of wetlands in the world is around 5%. The CH4 produced in the anaerobic zones of the sediments by methanogenic archaea can be oxidized to CO2 by the methanotrophic microorganisms. Based on the hypothesis that methane flux changes seasonally in wetlands and its microbiota is directly related to this process, this research has the main objective to evaluate the dynamics of the functional genes involved in the CH4 cycle in contrasting seasons, correlating with the CH4 flux, environmental variables and taxonomic profile of Bacteria and Archaea in three wetlands and one primary forest of the Eastern Amazon (Belterra and Santarém-PA). The sampling of gas, sediments and soil was performed in May and October 2016 (wet and dry seasons) to determine the concentration of CH4 retained in the sediment in the wet season, measurement of CH4 flux in the dry season, physicochemical properties and molecular analysis (qPCR of the mcrA, pmoA functional genes and phylogenetic marker genes 16S rRNA of Bacteria and Archaea and sequencing of the 16S rRNA gene of Bacteria and Archaea). From gas samplings, it was possible to observe that wetlands have the potential to act as source of CH4 during the wet season, and as a source or drain of CH4 during the dry season, confirmed by qPCR analyzes, due the abundance increases of the pmoA gene during the dry season. In the forest soil, the mcrA gene was not detected, therefore, the forest could be considered only as CH4 drain potential. The ACE estimator and the Shannon index showed that the sediments of wetlands have higher richness and diversity of Bacteria and Archaea when compared to the forest soil. All areas presented similar taxonomic profiles of Bacteria, however, the main difference between the communities is related to the Archaea. The archaeal community in the forest soil is mostly composed of representatives of the phylum Thaumarchaeota. The forest soil presented low abundance of the phyla with potential CH4 producers, Bathyarchaeota and Euryarchaeota, however the opposite was observed in the wetlands. The data generated in the present study encourage the continuity of work related to the CH4 cycle in wetlands of the Amazon basin, including investigations about the role of the Bathyarchaeota phylum in these areas, especially in relation to the CH4 cycle

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20953号 / 理博第4405号 / 新制||理||1633(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 中野 伸一, 教授 木庭 啓介, 教授 中川 尚史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

Keystone species are widely distributed across aquatic and terrestrial ecosystems and are fundamental in preserving the structure, diversity, and stability of an ecological community due to its disproportionately large impact on its community relative to its biomass. As biodiversity of ecosystems becomes more threatened with urbanization and habitat destruction, it is imperative to understand a keystone species' role in maintaining ecosystem function. One of the ways to do so is by examining their significance and connection to the ecosystem food web. Within North American freshwater ecosystems is the pebble nest-building minnow, the bluehead chub (Nocomis leptocephalus; "chub"). Chubs provide spawning habitat for not only themselves, but for other minnows, collectively called "nest associates". In this work, I observe the predatory and potential mutualistic interactions between chubs, nest associates, and their predators. In Chapter 1, I observe spawning nests to identify the predators of adult chubs, nest associates, and embryos. I further investigate how nest visibility covariates including minnow activity, minnow abundance, nest size (area), and nest growth affect predator encounter rate to spawning nests. I found a total of 23 diverse taxa to prey on the adult minnows and minnow embryos on chub spawning nests, 14 predators of which had not been reported in literature. One of these predators was the common snapping turtle (Chelydra serpentina; "turtle"). Additionally, I found that activity, abundance, nest size (area), and nest growth had a significant effect on predator encounter rate, attracting predators to seek spawning nests for prey. In Chapter 2, I investigate the effect of ambient temperature on turtle epizoic coverage during the spawning season and provide preliminary evidence of a potential cleaning symbiotic mutualism between the turtle and minnows. I found that epizoic coverage decreases during the duration of a minnow spawning season after an initial increase with early summer warming, and my results also present unique and shared bacterial communities across three sources, the ambient environment, gut contents of minnows, and turtles. The results additionally revealed there to be bacterial communities unique between minnows and turtles that were not identified in the ambient environment. Overall, this study is first to systematically document predators of chub spawning nests and first to provide preliminary evidence of a cleaning symbiotic mutualism between a freshwater turtle and minnow species (or freshwater turtles and fish in general), which, thus far, has not been explored in freshwater ecosystems. This work demonstrates that chub spawning nests are a crucial entity of the freshwater food web structure across Nocomis' distribution range and reveals that chub spawning nests create an interconnection between a diversity of fauna in a freshwater ecosystem. / Master of Science / Ecological communities often include species that are essential in ensuring the overall stability and biodiversity of an ecosystem. These species, otherwise called keystone species, play a crucial role in facilitating interconnections within the ecosystem's food web. The bluehead chub (Nocomis leptocephalus; "chub") is an example of a keystone minnow found in North American freshwater streams. This minnow engages in a complex, distinguished act when it reproduces, making mounded, pebble nests using only its mouth. Chubs are not the only minnow species interested in this engineering complexity. Various minnow species called "nest associates" reproduce on the nests as well, providing an appearance of a mutualism: all species involved benefit from the interaction. While this interaction has been observed, there is limited research identifying predators of chub nests and if there are potential mutualisms with any of these predators. In this work, I identify predatory and mutualistic interactions between chubs, nest associates, and their predators. In Chapter 1, I identify predators of chub nests and observe variables that attract these predators to the nests. In Chapter 2, I explore a potential, mutualistic interaction between these minnows and an identified predator from this research, the common snapping turtle (Chelydra serpentina; "turtle"), whereby minnows feed on potentially harmful growth of algae and bacteria on turtles, while turtles benefit from the cleaning. For Chapter 1, my results revealed that a chub nest is a hotspot for predator diversity, showing 23 diverse taxa as predators, in which 14 of the identified taxa are novel for ecological literature. Additionally, variables that were observed to attract predators to chub nests were minnow activity, minnow abundance, nest size (area), and nest growth. Results for Chapter 2 demonstrated that there are unique bacterial communities between turtles and minnows that are not found in the stream environment, therefore providing preliminary evidence of mutualistic interaction between the coexisting species. Overall, this study is the first to systematically document predators of chub nests. This study is also first to investigate a mutualistic interaction between minnows and turtles in a freshwater ecosystem, an area that has not been previously explored, unlike similar interactions in marine ecosystems. Cohesively, the keystone species, the chub, and their reproductive nests, are important for the aquatic food web structure and the interconnectedness to their overall ecosystem function. This research further stewards scientific knowledge about how important Nocomis are to natural freshwater ecosystems.

Integrating crop and livestock is being considered to improve soil health by carbon sequestration. A two-year study (2019-2021) at CPBES in Newton, MS was aimed to evaluate soil microbial diversity in the warm, humid regions, specifically southeastern USA. Amplicons targeting bacterial 16S rRNA genes and fungal ITS2 regions were sequenced. Taxonomic assignment and microbial diversity characterization were performed using QIIME2®. Soil fungal diversity showed significant differences (alpha diversity, p = 0.031 in yr. 2020 and beta diversity, p = 0.037 in yr. 2021). Canonical Correspondence Analysis (CCA) and Mantel test showed significant influence on fungal diversity due to carbon (rm = 0.2581, p = 0.022), nitrogen (rm = 0.2921, p = 0.0165) in yr. 2021, and on bacterial diversity due to EE-GRSP (rm = 0.22, p = 0.02) in yr. 2020. Long term study of ICLS can help us better understand the shift in microbiome to improve crop production sustainably.

Our understanding of microbial evolution is largely dependent on available genomic data of diverse organisms. Yet, genome-sequencing efforts have mostly ignored the diverse uncultivable majority in favor of cultivable and sociologically relevant organisms. In this thesis, I have applied and developed cultivation independent methods to explore microbial diversity and obtain genomic data in an unbiased manner. The obtained genomes were then used to study the evolution of mitochondria, Rickettsiales and Haloarchaea. Metagenomic binning of oceanic samples recovered draft genomes for thirteen novel Alphaproteobacteria-related lineages. Phylogenomics analyses utilizing the improved taxon sample suggested that mitochondria are not related to Rickettsiales but rather evolved from a proteobacterial lineage closely related to all sampled alphaproteobacteria. Single-cell genomics and metagenomics of lake and oceanic samples, respectively, identified previously unobserved Rickettsiales-related lineages. They branched early relative to characterized Rickettsiales and encoded flagellar genes, a feature once thought absent in this order. Flagella are most likely an ancestral feature, and were independently lost during Rickettsiales diversification. In addition, preliminary analyses suggest that ATP/ADP translocase, the marker for energy parasitism, was acquired after the acquisition of type IV secretion systems during the emergence of the Rickettsiales. Further exploration of the oceanic samples yielded the first draft genomes of Marine Group IV archaea, the closest known relatives of the Haloarchaea. The halophilic and generally aerobic Haloarchaea are thought to have evolved from an anaerobic methanogenic ancestor. The MG-IV genomes allowed us to study this enigmatic evolutionary transition. Preliminary ancestral reconstruction analyses suggest a gradual loss of methanogenesis and adaptation to an aerobic lifestyle, respectively. The thesis further presents a new amplicon sequencing method that captures near full-length 16S and 23S rRNA genes of environmental prokaryotes. The method exploits PacBio's long read technology and the frequent proximity of these genes in prokaryotic genomes. Compared to traditional partial 16S amplicon sequencing, our method classifies environmental lineages that are distantly related to reference taxa more confidently. In conclusion, this thesis provides new insights into the origins of mitochondria, Rickettsiales and Haloarchaea and illustrates the power of cultivation independent methods with respect to the study of microbial evolution.

Le microbiome de la rhizosphère fait généralement référence aux communautés bactériennes, archées et fongiques ainsi qu'à leur matériel génétique entourant étroitement les systèmes racinaires des plantes. Le métagénome de ce microbiome a été appelé le deuxième génome de la plante puisqu’elle est capable de profiter de plusieurs fonctions dont elle manque. La communauté microbienne de la rhizosphère inclue entre autres des microorganismes ayant développé des interactions intimes et spécifiques de longue durée avec les racines des plantes. Il s'agit d'une communauté dynamique de microorganismes, à partir de laquelle une partie d’espèces a développé des interactions intimes et spécifiques de longue durée avec les racines des plantes. Les progrès récents dans l’étude des interactions plantes-microbes ont démontré leur impact considérable sur la croissance, la nutrition et la santé des plantes. Le microbiote de la rhizosphère est complexe avec une structure spatio-temporelle dynamique qui s'adapte rapidement en fonction des stress biotiques et abiotiques. Considérant l’importance du microbiome de la rhizosphère pour la santé des plantes, des informations précises sur leurs microbes associés sont d'une importance capitale pour déchiffrer les mécanismes d'adaptation des plantes aux stress médiés par le microbiome et comprendre comment les plantes recrutent des taxons microbiens clés pour mieux faire face aux conditions stressantes. Pour ce faire, nous avons mené trois études afin de faire la lumière sur les facteurs qui jouent un rôle dans le recrutement et la structure du microbiome de la rhizosphère de plantes dans les milieux stressés. Dans un premier lieu, nous avons testé si des inoculations répétées avec des protéobactéries influençaient la productivité des plantes et les communautés microbiennes associées à la rhizosphère de quatre espèces végétales poussant dans des sédiments contaminés par des hydrocarbures pétroliers. Une expérience de mésocosme a été réalisée en conception de blocs randomisés avec deux facteurs : 1) la présence ou l'absence de quatre espèces végétales collectées dans un bassin de sédimentation d'une ancienne usine pétrochimique, et 2) l'inoculation ou non avec un consortium bactérien composé de dix isolats de Protéobactéries. Les plantes ont été cultivées en serre pendant quatre mois. Le séquençage d'amplicon MiSeq, ciblant le gène de l'ARNr 16S bactérien l’ITS fongique, a été utilisé pour évaluer les structures de la communauté microbienne des sédiments provenant de mesocosmes plantés ou non plantés. Nos résultats ont montré qu’alors que l'inoculation provoquait un changement significatif dans les communautés microbiennes, la présence de la plante et de son identité spécifique avait une influence plus forte sur la structure du microbiome dans les sédiments contaminés par les hydrocarbures pétroliers. Ensuite, en utilisant le même dispositif expérimental, nous avons utilisé le séquençage d'amplicon MiSeq ciblant le gène de l'ARNr 18S pour évaluer les structures communautaires AMF dans les racines et la rhizosphère de plantes poussant dans des substrats contaminés et non contaminés. Nous avons également étudié la contribution de l'identité spécifique des plantes et du biotope (racines des plantes et sol rhizosphérique) dans la formation des assemblages AMF associés. Nos résultats ont montré que si l'inoculation provoquait un changement significatif dans les communautés AMF, la contamination du substrat avait une influence beaucoup plus forte sur leur structure, suivie par le biotope et l'identité végétale dans une moindre mesure. De plus, l'inoculation augmentait considérablement la production de biomasse végétale et était associée à une diminution de la dissipation des hydrocarbures pétroliers dans le sol contaminé. Le résultat de cette étude fournit des connaissances sur les facteurs influençant la diversité et la structure communautaire de l'AMF associée aux plantes en milieux stressés à la suite d’inoculations répétées d'un consortium bactérien. Finalement, nous avons testé l’effet d’une inoculation d’arbres avec des champignons mycorhiziens spécifiques sur leur survie et croissance, ainsi que l’extraction de métaux traces. Pour ce faire, une expérience sur le terrain a été menée dans laquelle nous avons cultivé le clone de Salix miyabeana "SX67" sur le site d'une décharge industrielle déclassée, et inoculé les arbustes avec le champignon arbusculaire mycorhizien Rhizophagus irregularis, le champignon ectomycorhizien Sphaerosporella brunnea, ou un mélange des deux. Après deux saisons de croissance, les saules inoculés avec le champignon S. brunnea ont produit une biomasse significativement plus élevée. Le Ba, le Cd et le Zn se sont avérés être accumulés dans les parties aériennes des plantes, où le Cd présentait les valeurs de facteur de bioconcentration les plus élevées dans tous les traitements. De plus, les parcelles où les saules ont reçu l'inoculation de S. brunnea ont montré une diminution significative des concentrations de Cu, Pb et Sn dans le sol. L'inoculation avec R. irregularis ainsi que la double inoculation n'ont pas influencé de manière significative la production de biomasse et les niveaux d’éléments traces du sol. Le résultat de cette étude apporte des connaissances sur la diversité et l’écophysiologie des microbes de la rhizosphère associés aux plantes de croissance spontanée à la suite d’inoculations répétées. De plus ils montrent le potentiel de l’utilisation de champignons mycorhiziens afin d’améliorer la santé et croissance des plantes dans des milieux pollués et toxiques. Ils soulignent aussi l'importance de la sélection des plantes afin de faciliter leur gestion efficace et accélérer les processus de remise en état des terres. / The rhizosphere microbiome generally refers to the bacterial, archaea, and fungal communities and their genetic material that closely surrounds the root systems of plants. The metagenome of this microbiome has been called the second genome of the plant because it is able to take advantage of several functions that it lacks. It is a vibrant community of microorganisms, from which part of the species has developed long-lasting, specific and intimate interactions with plant roots. Recent advances in the study of plant-microbe interactions have demonstrated their considerable impact on plant growth, nutrition and health. The rhizosphere microbiota is complex with a dynamic spatio-temporal structure which adapts rapidly to biotic and abiotic stresses. Considering the importance of the rhizosphere microbiome to plant health, accurate information about their associated microbes is of utmost importance in deciphering the mechanisms of plant adaptation to microbiome-mediated stress, and understanding how plants recruit key microbial taxa to better cope with stressful conditions. To do this, we conducted three studies to shed light on the factors that play a role in the recruitment and structure of the microbiome of the rhizosphere of plants in stressed environments. First, we tested whether repeated inoculations with Proteobacteria influenced the productivity of plants and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was carried out in design of randomized blocks with two factors: 1) the presence or absence of four plant species collected in a sedimentation basin of a former petrochemical plant, and 2) inoculation or not with a bacterial consortium made up of ten isolates of Proteobacteria. The plants were grown in the greenhouse for four months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess the microbial community structures of sediments from planted and unplanted microcosms. Our results showed that while inoculation caused a significant change in microbial communities, the presence of the plant and its specific identity had a stronger influence on the structure of the microbiome in sediments contaminated with petroleum hydrocarbons. Next, using the same experimental setup, we used MiSeq amplicon sequencing targeting the 18S rRNA gene to assess AMF community structures in the roots and rhizosphere of plants growing in contaminated and uncontaminated substrates. We also studied the contribution of the specific identity of plants and the biotope (plant roots and rhizospheric soil) in the formation of associated AMF assemblages. Our results showed that while inoculation caused a significant change in AMF communities, substrate contamination had a much stronger influence on their structure, followed by biotope and plant identity to a lesser extent. In addition, inoculation dramatically increased plant biomass production and was associated with decreased dissipation of petroleum hydrocarbons in contaminated soil. The result of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with plants in stressed environments following repeated inoculations of a bacterial consortium. Finally, we tested the effect of inoculating trees with specific mycorrhizal fungi on their survival and growth, as well as the extraction of trace metals. To do this, a field experiment was carried out in which we cultivated the Salix miyabeana "SX67" clone on the site of a decommissioned industrial landfill and inoculated the shrubs with the arbuscular mycorrhizal fungus Rhizophagus irregularis, the ectomycorrhizal fungus Sphaerosporella brunnea, or a mixture of both. After two growing seasons, willows inoculated with the fungus S. brunnea produced a significantly higher biomass. Ba, Cd and Zn were found to accumulate in the aerial parts of plants, where Cd had the highest bioconcentration factor values in all treatments. In addition, the plots where the willows were inoculated with S. brunnea showed a significant decrease in the concentrations of Cu, Pb and Sn in the soil. The inoculation with R. irregularis as well as the double inoculation did not significantly influence the biomass production and the soil trace elements levels The result of this study provides insight into the diversity and ecophysiology of rhizosphere microbes associated with spontaneously growing plants following repeated inoculations. In addition, they show the potential of using mycorrhizal fungi to improve plant health and growth in polluted and toxic environments. They also stress the importance of plant selection to facilitate their efficient management, in order to speed up land reclamation processes.

Les plantes, par leurs racines, offrent une myriade de niches écologiques pour les microorganismes du sol, et ceux-ci la protègent contre les attaques parasitaires et les stress abiotiques, et favorisent son approvisionnement en nutriments et en eau. Cependant, dans le sol, la plante joue aussi un rôle important lorsqu’elle émet depuis ses racines des composés qui influencent la composition des communautés microbiennes dudit sol, ce combiné à un changement du pH du sol par la plante et son apport en matière organique ainsi qu’en oxygène. Ces composés influencent les membres du microbiote souterrain de la plante et donc indirectement la plante elle-même. Plus on a une diversité du couvert végétal, plus la diversité des microorganismes du sol va être élevée et inversement, plus un sol sera divers en matière de microbes plus les plantes qui y poussent tendent à être en bonne santé. Pour une plante en particulier, il n’est pas inhabituel de développer des relations spécifiques avec des microorganismes eux aussi spécifiques qui vont améliorer sa survie. Cependant, une plante peut vivre dans différents environnements et les sols sont divers, donc les plantes doivent s’adapter aux microbes qu’elles trouvent à proximité en sélectionnant les microbes les plus bénéfiques pour elles. Du coup, il est possible que quel que soit l’environnement dans lequel la plante pousse, quelques microbes soit si importants pour sa survie et son développement qu’on les retrouve toujours en association avec ladite plante. Ces microbes toujours en association avec une plante donnée constituent une unité théorique nommée core microbiote dans la littérature scientifique. La gestion du microbiote des plantes cultivées pourrait améliorer la résistance au stress et la productivité des plantes cultivées et il est donc important d’en comprendre le fonctionnement. A ce jour, le microbiote souterrain des plantes demeure largement une « boîte noire » en raison de son incroyable complexité due à la diversité faramineuse des microorganismes qui le constituent. Au cours de ma recherche doctorale, j’ai voulu participer à ouvrir encore un peu plus cette « boite noire » pour augmenter la connaissance du fonctionnement et de la structure du microbiote souterrain des plantes. Pour ce faire, j’ai utilisé le canola (B. napus) comme plante modèle. J’ai étudié le microbiote racinaire, tel qu’influencé par le niveau de diversification du système cultural, à l’aide d’un dispositif expérimental établi par Agriculture et Agroalimentaire Canada à cinq emplacements dans la prairie canadienne en 2008. Le canola, B. napus est une Brassicaceae économiquement importante, mais aussi intéressante en tant que plante modèle, car le canola est associé à des communautés microbiennes racinaire moins complexes que bien d’autres plantes, à cause de sa production de composés antimicrobiens. J’ai utilisé le séquençage d’amplicons, des analyses statistiques multivariées et l’analyse de réseau pour approcher cette complexité et: i) vérifier l’impact de la diversification du système de rotation cultural sur les communautés microbiennes souterraines du canola, ii) établir si un core microbiote fongique et bactérien existait bel et bien dans la rhizosphère du canola et le plein sol en culture de canola, iii) identifier de façon claire des espèces clef de voute interagissant intensivement dans les communautés fongiques, bactériennes, et mixtes, et finalement iv) évaluer la persistance des champignons mycorhiziens à arbuscules dans la rhizosphère du canola et le plein sol adjacent cette plante non-hôte, en systèmes culturaux basés sur le canola. Mes résultats confirment que les communautés fongiques de la rhizosphère du canola et de son sol étaient influencées par la diversification des rotations de cultures, mais démontrent que les communautés bactériennes ne l’étaient pas. La rhizosphère du canola avait un core microbiote fongique variant avec les années, tandis que chez les bactéries, seulement des core espèces ont été identifiées. J’ai aussi relevé des interactions potentielles entre microbiote fongique et microbiote bactérien du canola et identifié des espèces clef de voute. Les fluctuations de l’abondance de ces espèces pourraient alors faire varier celles de beaucoup d’autres microbes. Bradyrhizobium a été l’une de ces espèces. Mes résultats montrent aussi un maintien d’une communauté des champignons mycorhiziens à arbuscules chez le canola même après 10 ans de monoculture. En résumé, ma recherche apporte une lumière nouvelle dans l’étude du fonctionnement, de la structure et des dynamiques écologiques au sein du microbiote souterrain du canola et sur l’écologie microbienne théorique des plantes notamment en ce qui a trait à ses composantes invariantes telles que le core microbiote et les taxons clef de voûte. Des études en conditions contrôlées sont nécessaires pour vérifier la capacité des microbes clef de voute rapportés ici à influencer les communautés microbiennes du sol et les plantes qui y vivent. / Plants and soil microbes are closely linked. Plants provides myriads of ecological niches in and on its roots for microbes to thrive. In turn, microbes can protect host plants against pathogen attacks, abiotic stresses, and improve nutrient and water availability. In the distant soil, plant produce volatile compounds shaping microbial communities, with feedback on root-associated communities. The more diversity there is in the plant cover, the higher the diversity of soil microorganisms will be and conversely, the more diverse a soil will be in terms of microbes, the more de plants that grow there trend to be in good health. Certain plants can develop specific relationships with certain microbes improving the fitness of the plant. However, a plant can grow in different environments and soils are diverse, thus plant will have to adapt to the different microbes depending on the environment it is growing in while attracting the ones necessary for its growth. Certain microbes could be so important for a plant’s health and development that they are always associated with the plant. Such important microbes form a theoretical group called core microbiota that could be extremely important for plant health and a determinant of the composition of plant-associated microbial communities. The plant subterranean microbiota is often labelled as a “black box” due to the tremendous diversity and interactivity of the microbial communities plants host. In my thesis research I aimed to “crack the black box” a little further to enhance our understanding of plant subterranean microbial community dynamics and structure. To do so, I used a field experiment established in 2008 by Agriculture and Agri-Food Canada (AAFC) at five different sites in the Canadian Prairies under different crop rotations and canola as model plant. Canola (B. napus) is a crop plants of the Brassicaceae family that produces antimicrobial compounds and has “simpler” microbial community in its roots, and rhizosphere. To do so, I used amplicon sequencing, multivariate analysis, and network analysis. My objectives were i) to verify the impacts of plant cover diversification on canola microbial subterranean community, ii) to verify if a core microbiota of fungi and bacteria could exist in canola rhizosphere and bulk soil and if so, to describe this core, iii) to identify keystone bacteria and fungi, i.e. highly interacting components, in the bacterial and fungal communities associated with canola, and finally, iv) to investigate the persistence of arbuscular mycorrhizal fungi in the rhizosphere and bulk soil of canola, a non-host plant, in canola-based cropping systems. I found that the diversification of cropping systems influenced the structure of the fungal communities of canola rhizosphere and bulk soil, but diversification had no significant influence on bacterial community structure. A fungal core microbiota varying through years was found in canola rhizosphere, but no bacterial core-microbiota was found. However, we were able to identify a core-specie. Interactions among the fungal and bacterial microbiota in canola rhizosphere and bulk soil were found and Bradyrhizobium was among several potentially important keystone taxa. My results also show the maintenance of arbuscular mycorrhizal fungi in canola even after 10 years of monoculture despite this plant is not a host for AMF. Overall, my PhD research brings a new level of knowledge on the microbial structure and dynamics of canola subterranean microbiota, and also on the theoretical ecology of plant microbiota, particularly regarding its invariable components such as core microbiota and hub-taxa. Further investigations are needed to better understand how keystone species and core species influence the plants and their microbiome.

Le bleuet sauvage (Vaccinium angustifolium Ait. et V. myrtilloides Michaux) représente un marché en plein essor au Canada, premier pays producteur et exportateur mondial de ce fruit. Pour faire face à la demande, les producteurs cherchent continuellement à adapter leurs pratiques de production dans le but d’améliorer leur rendement et l'état de santé de leurs bleuetiers. Or, les micro-organismes présents dans les racines et dans le sol jouent un rôle non négligeable en lien avec la santé des plantes. Ce microbiote est donc d’intérêt d’un point de vue agronomique, pourtant, contrairement à d’autres cultures, très peu d’études se sont penchées spécifiquement sur le microbiote du milieu racinaire du bleuetier sauvage. Ce doctorat s’inscrit donc dans l’optique d’accroître les connaissances sur les communautés bactériennes et fongiques présentes dans les bleuetières au Québec. Les objectifs de ce projet sont de détecter les taxons qui pourraient avoir un impact sur les variables agronomiques des bleuetiers telles que le rendement; d’identifier les variables physico-chimiques du sol influençant ces communautés; et d’étudier les impacts que peuvent avoir les différentes pratiques agricoles, telles que la fertilisation et la fauche thermique, sur ces micro-organismes. Nous nous sommes appuyés sur le séquençage de nouvelle génération et le métacodage à barres de l’ADN environnemental de nos échantillons de racines et de sol afin d’obtenir une analyse des communautés bactériennes et fongiques de la rhizosphère et des racines des bleuetiers. Les analyses multivariées effectuées par la suite permettent de comparer ces communautés et de voir si certaines espèces sont spécifiques à une condition particulière. Dans l’ensemble, cette thèse a donc permis de caractériser les communautés fongiques et bactériennes du milieu racinaire du bleuetier sauvage in situ dans plusieurs bleuetières du Québec. De nombreuses espèces de champignons mycorhiziens éricoïdes ont été systématiquement identifiées dans les trois études et leur prédominance suggère leur importance pour le bleuetier sauvage. Nous avons également trouvé que l’ordre bactérien des Rhizobiales, connu pour sa capacité à fixer l’azote atmosphérique, occupait une part importante de la communauté bactérienne. Les études sur la fertilisation et la fauche thermique ont démontré que ces deux pratiques agricoles avaient peu d’impact significatif sur les communautés microbiennes étudiées. Enfin, cette thèse donne des pistes de réflexion sur la fixation d’azote par les communautés bactériennes et pose les premières bases pour des essais de bio-inoculation avec les espèces fongiques et bactériennes détectées ayant un potentiel impact bénéfique sur la culture des bleuets sauvages. / The wild blueberry (Vaccinium angustifolium Ait. and V. myrtilloides Michaux) market is booming in Canada, the world's leading producer and exporter of this fruit. In order to meet the demand, growers are constantly trying to adapt their production practices to improve their yields and the health of their blueberry fields. Micro-organisms present in the roots and in the soil play a significant role in the health of the plants. This microbiota is therefore of interest from an agronomic point of view, yet, contrary to other crops, very few studies have been conducted specifically on the microbiota of the root environment of wild blueberries. This doctoral project therefore aims at increasing our knowledge of the bacterial and fungal communities present in wild blueberry fields in Quebec. The objectives of this project are to detect taxa that could have an impact on agronomic variables of wild blueberry fields such as fruit yield; to identify soil physico-chemical variables influencing these communities; and to study the impacts that different agricultural practices, such as fertilization or thermal pruning, may have on these micro-organisms. We relied on next generation sequencing and metabarcoding of environmental DNA from our root and soil samples to obtain an analysis of the bacterial and fungal communities in the rhizosphere and roots of blueberry shrubs. Subsequent multivariate analyses allow us to compare these communities and see if certain species are specific to a particular condition. Overall, this thesis has characterized the fungal and bacterial communities in the root environment of wild blueberry in situ in several Quebec wild blueberry fields. Numerous species of ericoid mycorrhizal fungi were systematically identified in all three studies, and their predominance suggests their importance to wild blueberries. We also found that the bacterial order Rhizobiales, known for its ability to fix atmospheric nitrogen, occupied an important part of the bacterial community. Studies on fertilization and thermal mowing showed that these two agricultural practices have limited significant impacts on the microbial communities studied. Finally, this thesis provides insights into nitrogen fixation by bacterial communities and lays the groundwork for bio-inoculation trials with the fungal and bacterial species detected to have a potential beneficial impact on wild blueberry cultivation.